Introduction to RNA Seq Course
- Dhivya Arasappan
- Groves B Dixon
- Nathan Abell
- Marie E Strader
We will meet at FNT 1.104 from Monday - Friday 1-4pm for our classes.
You are strongly encouraged to attend in person, but if you would like to attend virtually, use this zoom link:
https://utexas.zoom.us/j/91424696609
Zoom Instructions:
Please make sure your zoom version is updated ( and that you have a zoom account )-- this is required to join a UT-sponsored Zoom session. See this link for more details about zoom requirements: https://zoom.its.utexas.edu/home
Other setup:
Please make sure you have an ssh client installed on your computer. All macs come with terminal, so no installation is required. For windows laptops, install putty and winSCP. You will also need a TACC account with multi factor authentication set up.
Course Overview
This is a course designed to give you an overview of RNA-Sequencing in a hands-on manner. It will comprise of lectures and guided tutorials. For the tutorials, we will be used a canned dataset, but a large part of the last class day will be devoted to practicing the techniques learned on your own dataset. This course has the following objectives:
- To teach you about the different options that are available to you when setting up a RNA-Seq study.
- To teach you about the different options that are available to you when analyzing a RNA-Seq dataset.
- To familiarize you with how the Texas Advanced Computing Center (TACC) can be used to simplify and speed up your data analysis.
- To familiarize you with some of the typically used RNA-Seq analyses methods.
- To provide a vocabulary to understand NGS and RNA-Seq terminology and to provide give you a starting point of where to begin you own data analysis, and enough experience that you can begin that analysis on your own.
Your Instructors
Name | Affiliation | Expertise | How to contact? |
|---|---|---|---|
| Dhivya Arasappan (Instructor) | CBRS | Unix, TACC, RNA-Seq, Single cell RNA-Seq, hybrid genome assembly, pacbio | darasappan@austin.utexas.edu or come to FNT1.206C |
Jackson Saigusa (Teaching Assistant) | CNS | Bulk RNA-Seq, R, Unix |
Day 1: Introduction to RNA-Seq
- Logistics-Day 1
- Part 1: Lecture: Introduction to RNA-Seq
- Part 2: Unix and TACC Refresher
- The Quickest Unix Refresher ever
- TACC Overview
- Part 3: Getting NGS data ready
- Day 1 take aways
- Overview of TACC Submission
Day 2: Read Mapping and Pseudomapping
- Logistics-Day 2
- Read Mapping
- Dhivya's suggestions for Mapping
- Day 2 take aways
Day 3: Testing for Differential Expression and Visualization
- Logistics-Day 3
- The Big Picture
- Part A: Differential expression of annotated genes/transcripts
- Part B: (OPTIONAL) The new tuxedo suite for finding novel transcripts
- DETOUR: Where to get publicly available RNA-Seq data
- Day 3 take aways
Day 4: Downstream Analysis of Differentially Expressed Genes and 3' Targeted RNA-Seq
- Part 1: GO Enrichment and Pathway Analysis
- Pathway Analysis
- (OPTIONAL) Gene Set Enrichment Analysis
- Part 2: Clustering using WGCNA
(OPTIONAL) Lecture: Example project downstream analysis
- Part 3: Lecture: Introduction to tag-seq (3' targeted sequencing)
- Day 4 take aways
Day 5: Single Cell RNA-Seq And Practice
- Introduction to Single Cell RNA-Seq
- Single Cell RNA-Seq R script and Data
- Introduction to CBRS offered pods
Extras
MANY THANKS
Many thanks to Dr. Scott Hunicke-Smith and Dr. Jeff Barrick who taught the first Introduction to NGS course at UT. Many slides and wiki pages have been borrowed and adapted from their initial course.
Also, thanks to Dennis Wylie, Anna Battenhouse, Benni Goetz who have also provided some material for this course
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